• Title, Summary, Keyword: mtDNA D-loop

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Effect of RFLP Marker of the Mitochondrial DNA D-Loop Region on Milk Production in Korean Cattle (한우 Mitochondrial DNA D-Loop 영역의 RFLP Marker가 산유량에 미치는 영향)

  • Chung Eui-Ryong;Chung Ku-Young
    • Food Science of Animal Resources
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    • v.25 no.2
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    • pp.218-225
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    • 2005
  • This study was performed to determine sequence variation and RFLP of the mt DNA D-loop region using Southern blot hybridization analysis and to develop mt DNA marker affecting milk production traits in Hanwoo cows. The PCR was used to amplify an 1142 bp fragment within the D-loop region of mt DNA using specific primers. Mt DNA were digested with seven restriction enzymes and hybridized using DIG-labeled D-loop probe. The mt DNA RFLP polymorphisms were observed in the four enzymes, BamHI, RsaI, XbaI and HpaII. Nucleotide substitutions were detected at positions 441 (G/C), 469 (T/C), 503 (C/T), 569 (G/A), 614 (C/A) and 644 (C/T) of the mt DNA D-loop region between two selected lines. Significant relationship between the XbaI RFLP type and breeding value was found(p<0.05). Cows with A type had higher estimated breeding values than those with B type (P<0.05) between high and low milk production lines. Therefore, the RFLP marker of mt DNA could be used as a selection assisted tool for individuals with high milk producing ability in Hanwoo.

Novel Mutations in the Displacement Loop of Mitochondrial DNA are Associated with Acute Lymphoblastic Leukemia: A Genetic Sequencing Study

  • Yacoub, Haitham Ahmed;Mahmoud, Wael Mahmoud;El-Baz, Hatim Alaa El-Din;Eid, Ola Mohamed;ELfayoumi, Refaat Ibrahim;Elhamidy, Salem Mohamed;Mahmoud, Maged M.
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.21
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    • pp.9283-9289
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    • 2014
  • Background: Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children and represents approximately 25% of cancer diagnoses among those younger than 15 years of age. Materials and Methods: This study investigated alterations in the displacement loop (d-loop) region of mitochondrial DNA (mtDNA) as a risk factor and diagnostic biomarker for early detection and diagnosis of acute lymphoblastic leukemia. Using mtDNA from 23 subjects diagnosed with acute lymphoblastic leukemia, the first 450 bp of the d-loop region were amplified and successfully sequenced. Results: This revealed 132 mutations at 25 positions in this region, with a mean of 6 alterations per subject. The d-loop alterations in mtDNA in subjects were all identified as single nucleotide polymorphisms in a homoplasmic distribution pattern. Mutant alleles were observed in all subjects with individual frequency rates of up to 95%. Thirteen mutant alleles in the d-loop region of mtDNA occurred with a high frequency. Novel alleles and locations were also identified in the d-loop of mtDNA as follows: 89 G insertions (40%), 95 G insertions (13%), 182 C/T substitutions (5%), 308 C insertions (19%), and 311 C insertions (80%). The findings of this study need to be replicated to be confirmed. Conclusions: Further investigation of the relationship between mutations in mitochondrial d-loop genes and incidence of acute lymphoblastic leukemia is recommended.

Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds

  • Zhang, Tao;Lu, Hongzhao;Chen, Chen;Jiang, Hai;Wu, Sanqiao
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.7
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    • pp.921-926
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    • 2012
  • In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

Detection of a Large White-Specific Duplication in D-loop Region of the Porcine MtDNA (돼지 mtDNA D-loop 지역의 Large White 특이 중복현상 탐지)

  • Kim, Jae-Hwan;Han, Sang-Hyun;Lee, Sung-Soo;Ko, Moon-Suk;Lee, Jung-Gyu;Jeon, Jin-Tae;Cho, In-Cheol
    • Journal of Life Science
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    • v.19 no.4
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    • pp.467-471
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    • 2009
  • The entire D-loop region of the porcine mitochondrial DNA (mtDNA) was amplified from six pig breeds (Landrace, Duroc, Large White, Korean native pig, Berkshire, and Hampshire) using a primer set designed on the basis of reported porcine mtDNA sequences. From analyses through cloning, DNA sequencing and multiple sequence alignment, an 11-bp (TAAAACACTTA) duplication was observed after known tandem repetition in the D-loop region, which promoted hetroplasmy in mtDNA. Although the existence of the 11-bp duplication has been previously reported in Duroc and Japanese native pigs, there have not been any attempts to know the characteristics of this duplication in other breeds so far. A 150 bp fragment containing the 11-duplication was amplified and typed by polyacrylamide gel electrophoresis (PAGE). All Large Whites had two duplication units and Duroc showed heteromorphic patterns, 11.2% (9/80) of the animals had the 11-bp duplication in total. On the other hand, Landrace, Berkshire, Hampshire and Korean native pigs were non-duplicated. This result showed that the 11-bp duplication could be used as a breed-specific DNA marker for distinguishing pure Landrace and Large White breeds.

Effect of Sequence Variation in Bovine Mitochondrial DNA D-loop Region on Economic Traits for Hanwoo (한우 경제형질에 미치는 Mitochondrial DNA D-loop 영역의 염기서열 변이효과)

  • Oh, J.D.;Yoon, D.H.;Kong, H.S.;Lim, H.J.;Lee, H.K.;Cho, B.W.;Hong, K.C.;Jeon, G.J.
    • Journal of Animal Science and Technology
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    • v.45 no.6
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    • pp.933-938
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    • 2003
  • This study was performed to analyse the sequences of variations of mtDNA D-loop and their effects on carcass traits in Hnawoo(Korean cattle). The resulting sequences were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty five polymorphic sites by nucleotide substitution were found in mtDNA of Hanwoo. The frequencies of positions at 169, 16042, 16093, 16119, 16255 and 16302 nt with high levels of sequence polymorphism were 0.891, 0.117, 0.109, 0.182, 0.197 and 0.117, respectively. The substitution effect at 169 and 16119 nt was found significant on marbling score. Also substitution effect at 169 and 16042 nt was highly significant(p〈0.01) on backfat. thickness. Polymorphism of mtDNA sequence in D-loop region could be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Hanwoo.

Effect of Sequence Variation in Mitochondrial DNA D-loop Region on Milk and Milk Fat Production in Holstein Cows (Holstein의 유량과 유지방 생산에 미치는 Mitochondrial DNA D-loop 영역의 염기 서열 변이 효과)

  • Oh J. D.;Kong H. S.;Lee H. K.;Jeon G. J.
    • Reproductive and Developmental Biology
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    • v.29 no.1
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    • pp.9-13
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    • 2005
  • This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.

Effect of Sequence Variation in Bovine Mitochondrial DNA D-Ioop Region on ~ilk Production for Hanwoo (한우 산유량에 미치는 Mitochondrial DNA D-loop영역의 염기서열 변이효과)

  • Kong, H.S.;Oh, J.D.;Lim, H.J.;Lee, H.K.;Jeon, G.J.;Yoon, D.H.;Jeon, G.J.;Choi, J.G.;Choi, Y.H.;Cho, B.W.
    • Journal of Animal Science and Technology
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    • v.46 no.5
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    • pp.729-734
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    • 2004
  • This study was performed to analyze the sequence variations of mtDNA D-loop and their effects on milk in Hanwoo(Korean cattle). The resulting sequences were compared with previously published sequences for other cattle breeds (GenBank JOI394). The Polymerase Chain Reaction was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty polymorphic sites by nucleotide substitution were found in mtDNA D-loop region of Hanwoo. The frequencies of positions at 8, 169, 16042, 16051, 16057, 16093, 16119, 16122, 16209, 16255 and 16302 nt with high levels of sequence polymorphism were 0.150, 0.950, 0.085, 0.138, 0.106, 0.085, 0.138, 0.212, 0.085, 0.148 and 0.180, respectively. The substitution effect at 16119(p<0.1) and 16185(p< 0.05) nt was found significant on milk production. Polymorphism of mtDNA sequence in D-Ioop region could be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Hanwoo.

Sequence and Genetic Variation of Mitochondrial DNA D-loop Region in Korean Cattle (한우 Mitochondrial DNA D-loop 영역의 염기서열 및 유전변이)

  • Chung, E.R.;Kim, W.T.;Kim, Y.S.;Lee, J.K.;Han, S.K.
    • Journal of Animal Science and Technology
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    • v.44 no.2
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    • pp.181-190
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    • 2002
  • This study was performed to determine sequences of the mt DNA D-loop region, including $tRNA^{Pro}$ and $tRNA^{Pre}$ and to analysis sequence variation polymorphism in Korean cattle. The resulting sequencies were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify an 1142bp between nucleotides 15061 and 404 within the D-loop region of mt DNA using specific primers. Korean cattle showed 24 polymorphic sites by nucleotide substitutions and insertions of single base pairs. About 50% of polymorphic sites were found in positions 16042 to 16122 with the most variable region. Among these polymorphic sites, variations at 16055, 16230 and 16260 bp were detected as new sequence variants in Korean cattle. These specific polymorphic sites have not been reported in the Japanese black cattle and European cattle. Therefore, mt DNA variants in the D-loop region may be used as genetic markers for specifying Korean cattle. The frequencies of positions 169, 16302, 16093, 16042, 16119 with a high level of sequence polymorphism were 0.81, 0.56, 0.56, 0.50 and 0.43, respectively. In comparison of genetic distances, Korean cattle showed the more closely to European cattle as Bos taurus than Bos indicus such as African and India breeds. In conclusion, these mt DNA sequence polymorphisms in the D-loop region for Korean cattle may be useful for the analysis of cytoplasmic genetic variation and associations with economic important traits and genetic analysis of maternal lineage.

Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

  • Sultana, H.;Seo, D.W.;Bhuiyan, M.S.A.;Choi, N.R.;Hoque, M.R.;Heo, K.N.;Lee, J.H.
    • Asian-Australasian Journal of Animal Sciences
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    • v.29 no.12
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    • pp.1688-1695
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    • 2016
  • The maternally inherited mitochondrial DNA (mtDNA) D-loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D-loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.

Multiple Maternal Origins of Korean Native Chicken Based on the mtDNA D-loop Variation (mtDNA D-loop 변이로 확인된 한국재래닭의 다양한 모계기원)

  • Cho, Chang-Yeon;Lee, Pung-Yeon;Ko, Yeoung-Gyu;Kim, Hak-Kyu;Park, Mi-Na;Yeon, Seung-Hum
    • Korean Journal of Poultry Science
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    • v.38 no.1
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    • pp.5-12
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    • 2011
  • In this study, we analyzed the mitochondrial DNA D-loop region of Korean native chicken to clarify their phylogenetic relationships, possible maternal origin and routes of introduction into Korea. A 1231-1232 bp DNA fragment from the mtDNA D-loop region was sequenced in 315 chickens from 11 populations, Thirty-five variable sites that defined 21 haplotyes were observed. In Korean native chicken, diversity accounted for 90% of the variation, little differentiation among the strains. The 21 haplotypes clustered into 5 clades which were A, B, C, D and E. These results indicate that Korean chickens were derived from China with multiple origins.